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Domestic flights arriving at Boston and Manchester are late 25 percent of the time, one of the worst records in the country, according to a report released today.

The combined on-time performance of Logan International Airport and Manchester-Boston Regional Airport from July 2008 to June 2009 ranked 78th out of 89 metropolitan areas in the nation, according to the report by the Brookings Institution Metropolitan Policy Program, a division of the Washington, D.C., nonprofit public policy organization that researches ways to improve metro areas.

This year’s performance is a 2 percent improvement from the same time period in 2008, but 4 percent worse than five years ago. The average time for delayed flights was just over an hour, a 20 percent improvement since 2004, according to the study.

The Massachusetts Port Authority, which runs Logan, has been working hard to improve the airport’s on-time performance, said spokesman Matthew Brelis. The airport has a new runway that has reduced wind delays, he said, as well as a new taxiway that saves on taxi times and the country’s only market-based congestion-management plan that is activated when airlines schedule more flights than the airport can handle.

But some things are beyond Massport’s control, Brelis said: “Flights to and from our most popular destinations must pass through the New York airspace, the most congested and delayed airspace in the country.’’

Manchester airport officials did not return calls seeking comment.

The Brookings study, titled “Expect Delays,’’ analyzed 19 years of data provided by the Bureau of Transportation Statistics on 109 big commercial airports. The study found that the nation’s airports overall are experiencing some of the longest delays in aviation history.

Five commercial airports in the New York and New Jersey metropolitan area had the worst on-time performance record, according to the study, with 34 percent of flights arriving an average of 69 minutes late. At Maine’s Portland International Jetport, 27 percent of flights were delayed by an average of 59 minutes, the third poorest record in the country. At Bradley International Airport, outside Hartford, and T.F. Green Airport, near Providence, 21 percent of flights didn’t come in on time. Salt Lake City International Airport had the best on-time record, with only 14 percent of its flights arriving an average of 50 minutes late.

In the study, Logan and Manchester were calculated together per the Bureau of Economic Analysis’s definition of the Boston metropolitan area. According to the Bureau of Transportation Statistics, Logan had 148,550 domestic departures from June ’08 to June ’09, while Manchester had 23,475.

Air passenger travel decreased in 2008, a trend that has continued into this year, and airlines have reduced the number of flights, which has boosted recent on-time performance. But as the economy gets stronger and more people start traveling next year, as the Federal Aviation Administration is forecasting, the percentage of late flights will keep inching up, according to the report.

The study is important because it shows a need to improve the performance of a major economic engine, said coauthor Adie Tomer.

“In an increasingly globalizing economy, the ability to connect to major metropolitan hubs and international destinations is critical for our long-term economic health and competitiveness,’’ Tomer said.

To improve airport efficiency, the study recommends that policy makers direct funds to reduce congestion at the country’s busiest airports, construct high-speed rail corridors in heavily traveled corridors, and accelerate the implementation of new technologies, such as a satellite-based air traffic control system.

“Now is the time for the government . . . to sit down and think about how we can make the system more efficient for when those passenger numbers start coming back,’’ Tomer said.